.gitignore

@@ -176,4 +176,3 @@ pyrightconfig.json
 # End of https://www.toptal.com/developers/gitignore/api/python
 
 autobigs-engine/*
-bioconda-recipes/*

.vscode/launch.json

@@ -4,13 +4,7 @@
     // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
     "version": "0.2.0",
     "configurations": [
-        {
+        
-            "name": "Python Debugger: Current File",
-            "type": "debugpy",
-            "request": "launch",
-            "program": "${file}",
-            "console": "integratedTerminal"
-        },
         {
             "name": "Python Debugger: Current File with Arguments",
             "type": "debugpy",

Jenkinsfile

@@ -11,8 +11,8 @@ pipeline {
             parallel {
                 stage("recipes repo") {
                     steps {
-                        sh 'git clone https://github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git'
+                        sh 'git clone https://github.com/Syph-and-VPD-Lab/bioconda-recipes.git'
-                        dir('auto-updated-bioconda-recipes') {
+                        dir('bioconda-recipes') {
                             sh 'git pull'
                             sh 'git pull origin update-autobigs-engine'
                             sh 'git checkout update-autobigs-engine'
@@ -28,21 +28,13 @@ pipeline {
         }
         stage("generate recipe") {
             steps {
-                sh 'grayskull pypi autoBIGS.engine --maintainers "Harrison Deng"'
+                sh 'grayskull pypi autobigs.engine --maintainers "Harrison Deng"'
-                sh 'python patch_recipe.py'
+                sh 'python scripts/adapt_names.py autobigs.engine'
-                sh 'cp -r autobigs-engine/* auto-updated-bioconda-recipes/recipes/autobigs-engine/.'
-            }
-        }
-        stage("lint") {
-            steps {
-                dir('auto-updated-bioconda-recipes') {
-                    sh 'bioconda-utils lint recipes/ --packages autobigs-engine'
-                }
             }
         }
         stage("build") {
             steps {
-                sh 'conda build bioconda-utils/recipes/autobigs-engine'
+                sh 'conda build autobigs-engine'
             }
         }
         stage("commit") {
@@ -50,9 +42,10 @@ pipeline {
                 TOKEN = credentials('github.com')
             }
             steps {
-                dir('auto-updated-bioconda-recipes') {
+                dir('bioconda-recipes') {
-                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../pypi_latest_ver.py autoBIGS.engine)."'
+                    sh 'cp -r ../autobigs-engine/* recipes/autobigs-engine/.'
-                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/auto-updated-bioconda-recipes.git update-autobigs-engine'
+                    sh 'git commit -a -m "Automatically updated autobigs-engine bioconda recipe to $(python ../scripts/package_latest_version.py autoBIGS.engine)."'
+                    sh 'git push https://${TOKEN}@github.com/Syph-and-VPD-Lab/bioconda-recipes.git update-autobigs-engine'
                 }
             }
         }

autobigs-cli/meta.yaml

@@ -0,0 +1,50 @@
+{% set name = "autoBIGS.cli" %}
+{% set version = "0.4.2" %}
+
+package:
+  name: {{ name|lower|replace(".", "-") }}
+  version: {{ version }}
+
+source:
+  url: https://pypi.org/packages/source/{{ name[0] }}/{{ name }}/autobigs_cli-{{ version }}.tar.gz
+  sha256: fc7bf6c604974796f5c8aae52fd9ab9924f5490f4f207a26be803217aae30c82
+
+build:
+  entry_points:
+    - autoBIGS = autobigs.cli.program:run
+  noarch: python
+  script: {{ PYTHON }} -m pip install . -vv --no-deps --no-build-isolation
+  number: 0
+  run_exports:
+    - {{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}
+
+requirements:
+  host:
+    - python >=3.12
+    - setuptools >=64
+    - setuptools-scm >=8
+    - pip
+  run:
+    - python >=3.12
+    - autobigs-engine
+
+test:
+  imports:
+    - autobigs
+  commands:
+    - pip check
+    - autoBIGS --help
+    - autoBIGS info -h
+    - autoBIGS st -h
+  requires:
+    - pip
+
+about:
+  home: https://github.com/RealYHD/autoBIGS.cli
+  summary: A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases.
+  license: GPL-3.0-or-later
+  license_file: LICENSE
+
+extra:
+  recipe-maintainers:
+    - Harrison Deng

bioconda-recipes

@@ -0,0 +1 @@
+Subproject commit bca9514062303e6470b9dbb628b02f76f8de258d

environment.yml

@@ -6,5 +6,3 @@ dependencies:
   - conda-build
   - grayskull
   - git
-  - bioconda-utils
-  - python=3.10.*

patch_recipe.py

@@ -1,103 +0,0 @@
-#!/usr/bin/env python3
-
-import argparse
-from os import fdopen, path
-import os
-import re
-import shutil
-from sys import argv
-import tempfile
-
-INDENTATION = "  "
-GRAYSKULL_OUTPUT_PATH = "autoBIGS.engine"
-RUN_EXPORTED_VALUE = r'{{ pin_subpackage( name|lower|replace(".", "-"), max_pin="x.x") }}'
-LICENSE_SUFFIX = "-or-later"
-HOME_PAGE = "https://github.com/Syph-and-VPD-Lab/autoBIGS.engine"
-
-def _calc_indentation(line: str):
-    return len(re.findall(INDENTATION, line.split(line.strip())[0])) if line != "\n" else 0
-
-def read_grayskull_output():
-    original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
-    original_meta = path.join(original_recipe, "meta.yaml")
-    meta_file = open(original_meta)
-    lines = meta_file.readlines()
-    meta_file.close()
-    return lines
-
-def update_naming_scheme(lines):
-    modified_lines = []
-    for line in lines:
-        matches = re.finditer(r"\{\{\s*name\|lower()\s+\}\}", line)
-        modified_line = line
-        for match in matches:
-            modified_line = modified_line[:match.start(1)] + r'|replace(".", "-")' + modified_line[match.end(1):]
-        modified_lines.append(modified_line)
-    return modified_lines
-
-def inject_run_exports(lines: list[str]):
-    package_indent = False
-    modified_lines = []
-    for line in lines:
-        indentation_count = _calc_indentation(line)
-        if line == "build:\n" and indentation_count == 0:
-            package_indent = True
-            modified_lines.append(line)
-        elif package_indent and indentation_count == 0:
-            modified_lines.append(INDENTATION*1 + "run_exports:\n")
-            modified_lines.append(INDENTATION*2 + "- " + RUN_EXPORTED_VALUE + "\n")
-            package_indent = False
-        else:
-            modified_lines.append(line)
-    return modified_lines
-
-def suffix_license(lines: list[str]):
-    about_indent = False
-    modified_lines = []
-    for line in lines:
-        indentation_count = _calc_indentation(line)
-        if line == "about:\n" and indentation_count == 0:
-            about_indent = True
-            modified_lines.append(line)
-        elif about_indent and indentation_count == 1 and line.lstrip().startswith("license:"):
-            modified_lines.append(line.rstrip() + LICENSE_SUFFIX  + "\n")
-            about_indent = False
-        else:
-            modified_lines.append(line)
-    return modified_lines
-
-def inject_home_page(lines: list[str]):
-    about_indent = False
-    modified_lines = []
-    for line in lines:
-        indentation_count = _calc_indentation(line)
-        if line == "about:\n" and indentation_count == 0:
-            about_indent = True
-            modified_lines.append(line)
-        elif about_indent and indentation_count == 0:
-            modified_lines.append(INDENTATION + "home: " + HOME_PAGE + "\n")
-            about_indent = False
-        else:
-            modified_lines.append(line)
-    return modified_lines
-
-def write_to_original(lines: list[str]):
-    original_recipe = path.abspath(GRAYSKULL_OUTPUT_PATH)
-    original_meta = path.join(original_recipe, "meta.yaml")
-    with open(original_meta, "w") as file:
-        file.writelines(lines)
-
-def rename_recipe_dir():
-    new_recipe_name = path.abspath(path.join(GRAYSKULL_OUTPUT_PATH.replace(".", "-").lower()))
-    shutil.rmtree(new_recipe_name, ignore_errors=True)
-    os.replace(path.abspath(GRAYSKULL_OUTPUT_PATH), new_recipe_name)
-
-if __name__ == "__main__":
-    original_grayskull_out = read_grayskull_output()
-    modified_recipe_meta = None
-    modified_recipe_meta = update_naming_scheme(original_grayskull_out)
-    modified_recipe_meta = inject_run_exports(modified_recipe_meta)
-    modified_recipe_meta = suffix_license(modified_recipe_meta)
-    modified_recipe_meta = inject_home_page(modified_recipe_meta)
-    write_to_original(modified_recipe_meta)
-    rename_recipe_dir()

scripts/adapt_names.py

@@ -0,0 +1,32 @@
+#!/usr/bin/env python3
+
+import argparse
+from os import fdopen, path
+import os
+import re
+import shutil
+from sys import argv
+import tempfile
+
+def update_naming_scheme(recipe_path):
+    original_recipe = path.abspath(recipe_path)
+    original_meta = path.join(original_recipe, "meta.yaml")    
+    new_fd, new_file_path = tempfile.mkstemp()
+    with fdopen(new_fd, "w") as new_file_handle:
+        with open(original_meta, "r") as original_file_handle:
+            for line in original_file_handle:
+                matches = re.finditer(r"\{\{\s*name\|lower()\s+\}\}", line)
+                modified_line = line
+                for match in matches:
+                    modified_line = modified_line[:match.start(1)] + r'|replace(".", "-")' + modified_line[match.end(1):]
+                new_file_handle.write(modified_line)
+    shutil.move(new_file_path, original_meta)
+    new_recipe_name = path.join(
+                    path.dirname(original_recipe),
+                    path.basename(original_recipe).replace(".", "-").lower())
+    shutil.rmtree(new_recipe_name, ignore_errors=True)
+    os.replace(original_recipe, 
+                new_recipe_name)
+
+if __name__ == "__main__":
+    update_naming_scheme(argv[1])

scripts/package_latest_version.py

@@ -8,7 +8,6 @@ try:
 except ImportError:
     from pip._vendor.packaging.version import parse
 
-# Courtesy of https://stackoverflow.com/questions/28774852/pypi-api-how-to-get-stable-package-version
 
 URL_PATTERN = 'https://pypi.python.org/pypi/{package}/json'